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/*******************************************************************************
* $Id: MatchHashEntry.cpp,v 1.9 2004/03/01 02:40:08 darling Exp $
* This file is copyright 2002-2007 Aaron Darling and authors listed in the AUTHORS file.
* Please see the file called COPYING for licensing, copying, and modification
* Please see the file called COPYING for licensing details.
* **************
******************************************************************************/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libMems/MatchHashEntry.h"
#include "libGenome/gnException.h"
#include "libGenome/gnDebug.h"
using namespace std;
using namespace genome;
namespace mems {
boolean MatchHashEntry::offset_lessthan(const MatchHashEntry& a, const MatchHashEntry& b){
return a.m_offset < b.m_offset;
}
boolean MatchHashEntry::start_lessthan_ptr(const MatchHashEntry* a, const MatchHashEntry* b){
int32 start_diff = a->FirstStart() - b->FirstStart();
if(start_diff == 0){
uint32 m_count = a->SeqCount();
m_count = m_count <= b->SeqCount() ? m_count : b->SeqCount();
for(uint32 seqI = seq_compare_start; seqI < m_count; seqI++){
int64 a_start = a->Start(seqI), b_start = b->Start(seqI);
if(a_start < 0)
a_start = -a_start + a->Length() - a->m_mersize;
if(b_start < 0)
b_start = -b_start + b->Length() - b->m_mersize;
int64 diff = a_start - b_start;
if(a_start == NO_MATCH || b_start == NO_MATCH)
continue;
else if(diff == 0)
continue;
else
return diff < 0;
}
}
return start_diff < 0;
}
boolean MatchHashEntry::strict_start_lessthan_ptr(const MatchHashEntry* a, const MatchHashEntry* b){
int start_diff = a->FirstStart() - b->FirstStart();
if(start_diff == 0){
uint m_count = a->SeqCount();
m_count = m_count <= b->SeqCount() ? m_count : b->SeqCount();
for(uint seqI = 0; seqI < m_count; seqI++){
int64 a_start = a->Start(seqI), b_start = b->Start(seqI);
if(a_start < 0)
a_start = -a_start + a->Length() - a->m_mersize;
if(b_start < 0)
b_start = -b_start + b->Length() - b->m_mersize;
int64 diff = a_start - b_start;
if(diff == 0)
continue;
else
return diff < 0;
}
}
return start_diff < 0;
}
//ignores mem_no_matches
int64 MatchHashEntry::start_compare(const MatchHashEntry& a, const MatchHashEntry& b){
uint m_count = a.SeqCount();
m_count = m_count <= b.SeqCount() ? m_count : b.SeqCount();
for(uint seqI = 0; seqI < m_count; seqI++){
int64 a_start = a.Start(seqI), b_start = b.Start(seqI);
if(a_start < 0)
a_start = -a_start + a.Length() - a.m_mersize;
if(b_start < 0)
b_start = -b_start + b.Length() - b.m_mersize;
int64 diff = a_start - b_start;
if(a_start == NO_MATCH || b_start == NO_MATCH)
continue;
else if(diff == 0)
continue;
else
return diff;
}
return 0;
}
int64 MatchHashEntry::end_to_start_compare(const MatchHashEntry& a, const MatchHashEntry& b){
MatchHashEntry tmp_a = a;
tmp_a.CropStart(tmp_a.Length()-1);
return MatchHashEntry::start_compare(tmp_a, b);
}
MatchHashEntry::MatchHashEntry() :
Match(),
m_extended( false ),
m_mersize( 0 )
{
}
MatchHashEntry::MatchHashEntry(uint32 seq_count, const gnSeqI mersize, MemType m_type) :
Match( seq_count ),
m_mersize( mersize )
{
m_extended = m_type == extended;
}
MatchHashEntry* MatchHashEntry::Clone() const{
return new MatchHashEntry(*this);
}
MatchHashEntry& MatchHashEntry::operator=(const MatchHashEntry& mhe)
{
Match::operator=( mhe );
m_extended = mhe.m_extended;
m_mersize = 0;
m_offset = mhe.m_offset;
return *this;
}
boolean MatchHashEntry::operator==(const MatchHashEntry& mhe) const
{
if(m_seq_count != mhe.m_seq_count)
return false;
if(m_mersize != mhe.m_mersize)
return false;
if(m_extended != mhe.m_extended)
return false;
if( m_offset != mhe.m_offset )
return false;
return Match::operator ==(mhe);
}
void MatchHashEntry::CalculateOffset()
{
if( SeqCount() == 0 )
return;
int64 tmp_off = 0;
m_offset = 0;
uint seqI = FirstStart();
int64 ref_start = Start(seqI);
for(seqI++; seqI < SeqCount(); seqI++){
if(Start(seqI) != NO_MATCH){
tmp_off = Start(seqI) - ref_start;
if( Start(seqI) < 0 )
tmp_off -= (int64)Length( seqI );
m_offset += tmp_off;
}
}
}
// checks if mhe is _perfectly_ contained in this match.
// all offsets in all sequences must be aligned to each other
boolean MatchHashEntry::Contains(const MatchHashEntry& mhe) const{
uint i;
int64 diff_i;
int64 diff;
uint seq_count = mhe.SeqCount();
//check for a consistent number of genomes and
//identical generalized offsets
if(SeqCount() != seq_count || m_offset != mhe.m_offset)
return false;
i = mhe.FirstStart();
diff = mhe.Start(i) - Start(i);
if(Start(i) == NO_MATCH)
return false;
//check for containment properties
if(diff < 0 || Length() < mhe.Length() + diff)
return false;
//everything is ok so far, check for alignment
int64 diff_rc = (int64)mhe.Length() - (int64)Length() + diff;
for(i++; i < seq_count; i++){
//check for consistent alignment between all genomes
//in the case of revcomp, diff_i must equal diff_rc
diff_i = mhe.Start(i) - Start(i);
//it's ok if neither matches in a sequence
if(mhe.Start(i) == NO_MATCH && Start(i) == NO_MATCH)
continue;
else if(mhe.Start(i) < 0 && diff_rc == diff_i)
continue;
else if(diff != diff_i )
return false;
}
//it was contained.
return true;
}
} // namespace mems
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